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- EMDB-61606: Cryo-EM structure of the SE-PangolinCoV (MjHKU4r-CoV-1) RBD in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-61606
TitleCryo-EM structure of the SE-PangolinCoV (MjHKU4r-CoV-1) RBD in complex with human DPP4
Map data
Sample
  • Complex: SE-PangolinCoV-RBD (MjHKU4r-CoV-1):human DPP4 complex
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
    • Protein or peptide: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / VIRAL PROTEIN
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / Fc-gamma receptor I complex binding / chemorepellent activity / psychomotor behavior / intercellular canaliculus ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / Fc-gamma receptor I complex binding / chemorepellent activity / psychomotor behavior / intercellular canaliculus / complement-dependent cytotoxicity / dipeptidyl-peptidase activity / IgG immunoglobulin complex / peptide hormone processing / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / locomotory exploration behavior / lamellipodium membrane / FCGR activation / endocytic vesicle / complement activation, classical pathway / behavioral fear response / Role of phospholipids in phagocytosis / endothelial cell migration / aminopeptidase activity / antigen binding / receptor-mediated endocytosis of virus by host cell / T cell costimulation / serine-type peptidase activity / FCGR3A-mediated IL10 synthesis / T cell activation / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / antibacterial humoral response / lamellipodium / virus receptor activity / protease binding / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / response to hypoxia / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / membrane raft / endocytosis involved in viral entry into host cell / symbiont entry into host cell / signaling receptor binding / lysosomal membrane / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / focal adhesion / fusion of virus membrane with host endosome membrane / positive regulation of cell population proliferation / viral envelope / host cell plasma membrane / virion membrane / cell surface / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion ...Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Alpha/Beta hydrolase fold / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Immunoglobulin heavy constant gamma 1 / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesPangolin coronavirus HKU4/P251T/pangolin/2018 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsYuan H / Xiong X
Funding support3 items
OrganizationGrant numberCountry
Other governmentSRPG22-002
Other government2021YFA1300903
Other government2022A1515110495
CitationJournal: To Be Published
Title: The complex of SE-PangolinCoV-RBD and human DPP4
Authors: Yuan H / Xiong X
History
DepositionSep 20, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61606.png

Downloads & links

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Map

FileDownload / File: emd_61606.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 252 pix.
= 221.76 Å		0.88 Å/pix.
x 252 pix.
= 221.76 Å		0.88 Å/pix.
x 252 pix.
= 221.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.828233 - 5.2427597
Average (Standard dev.)0.000660533 (±0.15184496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 221.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61606_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61606_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : SE-PangolinCoV-RBD (MjHKU4r-CoV-1):human DPP4 complex

EntireName: SE-PangolinCoV-RBD (MjHKU4r-CoV-1):human DPP4 complex
Components
  • Complex: SE-PangolinCoV-RBD (MjHKU4r-CoV-1):human DPP4 complex
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
    • Protein or peptide: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SE-PangolinCoV-RBD (MjHKU4r-CoV-1):human DPP4 complex

SupramoleculeName: SE-PangolinCoV-RBD (MjHKU4r-CoV-1):human DPP4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pangolin coronavirus HKU4/P251T/pangolin/2018

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Macromolecule #1: Dipeptidyl peptidase 4 soluble form

MacromoleculeName: Dipeptidyl peptidase 4 soluble form / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.76357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLASRKTYT LTDYLKNTYR LKLYSLRWIS DHEYLYKQEN NILVFNAEYG NSSVFLENST FDEFGHSIN DYSISPDGQF ILLEYNYVKQ WRHSYTASYD IYDLNKRQLI TEERIPNNTQ WVTWSPVGHK LAYVWNNDIY V KIEPNLPS ...String:
MPMGSLQPLA TLYLLGMLVA SVLASRKTYT LTDYLKNTYR LKLYSLRWIS DHEYLYKQEN NILVFNAEYG NSSVFLENST FDEFGHSIN DYSISPDGQF ILLEYNYVKQ WRHSYTASYD IYDLNKRQLI TEERIPNNTQ WVTWSPVGHK LAYVWNNDIY V KIEPNLPS YRITWTGKED IIYNGITDWV YEEEVFSAYS ALWWSPNGTF LAYAQFNDTE VPLIEYSFYS DESLQYPKTV RV PYPKAGA VNPTVKFFVV NTDSLSSVTN ATSIQITAPA SMLIGDHYLC DVTWATQERI SLQWLRRIQN YSVMDICDYD ESS GRWNCL VARQHIEMST TGWVGRFRPS EPHFTLDGNS FYKIISNEEG YRHICYFQID KKDCTFITKG TWEVIGIEAL TSDY LYYIS NEYKGMPGGR NLYKIQLSDY TKVTCLSCEL NPERCQYYSV SFSKEAKYYQ LRCSGPGLPL YTLHSSVNDK GLRVL EDNS ALDKMLQNVQ MPSKKLDFII LNETKFWYQM ILPPHFDKSK KYPLLLDVYA GPCSQKADTV FRLNWATYLA STENII VAS FDGRGSGYQG DKIMHAINRR LGTFEVEDQI EAARQFSKMG FVDNKRIAIW GWSYGGYVTS MVLGSGSGVF KCGIAVA PV SRWEYYDSVY TERYMGLPTP EDNLDHYRNS TVMSRAENFK QVEYLLIHGT ADDNVHFQQS AQISKALVDV GVDFQAMW Y TDEDHGIASS TAHQHIYTHM SHFIKQCFSL PHHHHHH

UniProtKB: Dipeptidyl peptidase 4

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Macromolecule #2: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1

MacromoleculeName: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.018477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTCLTCLLMF LLMFVKDCDE AAATGTFIEQ PKSKECDFTP MLVGVPPQVY NFKRLVFTNC NYNLTKLLSL FMVNEFSCNG ISPDAIARG CYSSLTVDYF AYPLSMRSYI QPGSAGDISL YNYKQSFANP TCRVLATAPA NLTLTKPSAY GYFQKCSRVS G EHNSVETP ...String:
MTCLTCLLMF LLMFVKDCDE AAATGTFIEQ PKSKECDFTP MLVGVPPQVY NFKRLVFTNC NYNLTKLLSL FMVNEFSCNG ISPDAIARG CYSSLTVDYF AYPLSMRSYI QPGSAGDISL YNYKQSFANP TCRVLATAPA NLTLTKPSAY GYFQKCSRVS G EHNSVETP LYINPGEYSI CRSFSPYGFS EDGEVFRRQL TQYEGGGILV GVGAKLAMTD KLEMGFIISV QYGTDTNSVC PM LDLGNSS TITHYLGKCV DYDPLVPRGS GGGGDPEPKS CDKTHTCPPC PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCV VVDVSH EDPEVKFNWY VDGVEVHNAK TKPREEQYNS TYRVVSVLTV LHQDWLNGKE YKCKVSNKAL PAPIEKTISK AKGQ PREPQ VYTLPPSRDE LTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNV FSCS VMHEALHNHY TQKSLSLSPG K

UniProtKB: Spike glycoprotein, Immunoglobulin heavy constant gamma 1

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4kr0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 721281
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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